The molecular arrangement of copper phthalocyanine (CuPc) crystals on hydrogen-terminated Si(lll) surfaces was investigated by using both scanning probe microscopy and x-ray diffraction in terms of influence of the surface roughness, On a rough surface with a root-mean-square roughness of 0.20 nm, the molecules were stacked so as to form an a crystal where the molecular column was parallel to the surface. On the other hand, a new crystal form with its column exactly perpendicular to the Si(lll) plane was grown on a atomically flat surface. In this case, the molecules were stacked perpendicular to the substrate with the underlying molecules situated directly below. These molecular arrangements were independent of the growth temperature in the range of 60-180 degrees C. On the atomically flat surfaces, the strong interactive force between the surface and the planar CuPc molecule may result in the new growth behavior.